UCSC is fine with me, and I don't even need to fly to get there. I'm also extremely happy if they and/or Mark Diekhans will take this on. Much easier for me to simply attend - I just wanted to be sure that the meeting happens.
In my head I was thinking of this largely as a developer's meeting/workshop for coordinating efforts. -S On Feb 11, 2011, at 3:13 PM, Ann Loraine wrote: > I think it would be very helpful to have a meeting at UCSC. > > UCSC is such an important data provider that it would be good for all of us > to have more interactions with the team there. > > Very best wishes, > > Ann > > > On 2/9/11 9:19 AM, "Andy Jenkinson" <[email protected]> wrote: > >> Hi guys, >> >> Just to mention, Mark Diekhans has kindly offered to help us arrange >> something >> at UCSC if we want, so we can consider that a solid offer. I shall defer to >> the Wisdom Of The List as to preference for location (no doubt Suzi would >> prefer Berkeley!). I'm not sure if the aim is to attract participation or >> just >> get together. Also, what sort of dates are people thinking of? >> >> Cheers, >> Andy >> >> On 8 Feb 2011, at 21:49, Suzanna Lewis wrote: >> >>> >>> On Feb 8, 2011, at 2:44 PM, David Nix wrote: >>> >>>> There are several of us here who are planning on attending with probably 2 >>>> talks and or posters (GenoPub, GNomEx and BST). Would be nice to have a >>>> talk >>>> on just DAS (history, apps, data sources, advantages/ disadvantages, DAS/1 >>>> vs DAS/2, future directions, etc.) even if the DAS workshop doesn't >>>> materialize. >>>> >>>> Would someone who knows Tim or Alex be willing to approach them and inquire >>>> about the feasibility of a DAS workshop? >>> who? I probably should know who you're talking about, but they aren't part >>> of >>> the GI meeting or part of CSHL so ... >>> >>>> >>>> Suzi any more thoughts on a Bay Area session? >>> >>> Given enough lead time there is a good room I can reserve for holding the >>> meeting. So I suppose all that needs to be done at this point is for me to >>> check availability of this room and given that, set up a doodle poll. >>> >>> I'm assuming no more than 40 people. >>> >>>> >>>> -cheers, D >>>> >>>> >>>> On 2/7/11 11:02 AM, "Ann Loraine" <[email protected]> wrote: >>>> >>>> Hi, >>>> >>>> Ting Wang is senior author on a Nature Methods review article (March 2010) >>>> discussing visualization software for genomics. >>>> >>>> The dates: >>>> >>>> GENOME INFORMATICS >>>> November 2 - 5, 2011 >>>> Abstract Deadline: August 12, 2011 >>>> >>>> I have a break from teaching in the fall so I will definitely try to >>>> attend. >>>> >>>> The session on alternative splicing also looks very interesting. >>>> >>>> Who in the developer's list is interested in attending, contributing to an >>>> abstract, giving a talk? >>>> >>>> Best wishes, >>>> >>>> Ann >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> On 2/7/11 11:58 AM, "David Nix" <[email protected]> wrote: >>>> >>>>> Hmm... >>>>> >>>>> There's the Genome Informatics meeting in August at CSHL ( >>>>> http://meetings.cshl.edu/meetings/info11.shtml). It's not the bay area >>>>> and >>>>> the organizers might already have a set program. There is a "Databases, >>>>> Data >>>>> Mining, Visualization and Curation" session by Alex Bateman and Ting Wang >>>>> though. >>>>> >>>>> -cheers, D >>>>> >>>>> >>>>> >>>>> >>>>> On 2/7/11 9:25 AM, "Ann Loraine" <[email protected]> wrote: >>>>> >>>>> Hi, >>>>> >>>>> Same for us here at UNC Charlotte. >>>>> >>>>> Meetings I'm attending next include two major plant science meetings >>>>> (Arabidopsis and ASPB) and possibly ISMB in Vienna. >>>>> >>>>> David are there any other meetings you and your group are planning to >>>>> attend? >>>>> >>>>> The ideal setting would be a meeting where we can do outreach and hold >>>>> workshop event(s) for users, but also have a developers meeting where we >>>>> discuss future directions for the software, DAS spec, etc. >>>>> >>>>> Are there other meetings that would be a good fit? >>>>> >>>>> Best, >>>>> >>>>> Ann >>>>> >>>>> On 2/7/11 10:58 AM, "David Nix" <[email protected]> wrote: >>>>> >>>>>> Ah, that makes sense. >>>>>> >>>>>> As for a US meeting, there are 3 or 4 folks here at the U of Utah that >>>>>> would >>>>>> attend an out of state meeting. The bay area would be ideal (thanks >>>>>> Suzi!). >>>>>> It might be best to make this part of a larger genomics/ proteomics >>>>>> meeting >>>>>> to >>>>>> start. This would draw more folks who are interested in distributing >>>>>> their >>>>>> own data and working DAS access into their own applications. Are their >>>>>> any >>>>>> appropriate upcoming meetings? >>>>>> >>>>>> -cheers, D >>>>>> >>>>>> >>>>>> On 2/4/11 1:57 PM, "Andy Jenkinson" <[email protected]> wrote: >>>>>> >>>>>> Hi David, >>>>>> >>>>>> I guess one of the big reasons to want a proxy is it allows you to use >>>>>> DAS >>>>>> sources you don't control, which is obviously potentially a really big >>>>>> benefit >>>>>> with so many DAS/1 sources around. I don't know if this is what Jim is >>>>>> trying >>>>>> to achieve though. In truth this has always been the difficulty with the >>>>>> das/das2 tech divide really, with such a huge existing implementation >>>>>> base >>>>>> there's a very high "activation energy" in switching! >>>>>> >>>>>> What was the issue with the ensembl servers? >>>>>> >>>>>> Jon and I have talked a few times about organising a DAS workshop in >>>>>> North >>>>>> America, we just need someone to host (and to an extent fund) it. Do you >>>>>> have >>>>>> any suggestions? Almost all of the attendees for our workshops are from >>>>>> Europe, in fact lots are from Hinxton. So what sort of demand do you >>>>>> think >>>>>> there would be stateside for such an event? Enough for a standalone >>>>>> workshop, >>>>>> or more conducive to an add-on to or collaboration with another event? >>>>>> >>>>>> Maybe we can look into webcasting the talks? No idea how to go about this >>>>>> though! >>>>>> >>>>>> On 4 Feb 2011, at 19:13, David Nix wrote: >>>>>> >>>>>>> Hello Jim, >>>>>>> >>>>>>> If I make a suggestion. If you're looking to visualize genomic data in >>>>>>> IGB, >>>>>>> it would be best to use a DAS/2 server such as the Classic (command >>>>>>> line) >>>>>>> or >>>>>>> GenoPub (web app/ relational database) GenoViz DAS/2 server. DAS/2 is >>>>>>> well >>>>>>> suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, >>>>>>> bar, >>>>>>> useq...) and alignment data (ie BAM) to client apps. We're continuing >>>>>>> to >>>>>>> develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so >>>>>>> expect continuing improvements (bulk uploading and file conversion, >>>>>>> annotation via ontologies, super group visibility settings, additional >>>>>>> file >>>>>>> formats, etc.). See >>>>>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2 and our >>>>>>> paper >>>>>>> http://www.biomedcentral.com/1471-2105/11/455 >>>>>>> >>>>>>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz >>>>>>> DAS/2 >>>>>>> server supports DAS xml datasets so moving data from a DAS/1 server to >>>>>>> DAS/2 >>>>>>> wouldn't require any data reformatting. Although for large datasets, >>>>>>> it's >>>>>>> best to use one of the compressed binary data formats such as bar, bam, >>>>>>> or >>>>>>> useq. >>>>>>> >>>>>>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers. This >>>>>>> works >>>>>>> well for accessing their small annotation datasets (gene models: refseq, >>>>>>> knowngenes), but the graph distribution wasn't functional the last I >>>>>>> checked. >>>>>>> The problem appeared to be from the server side. >>>>>>> >>>>>>> -cheers, David >>>>>>> >>>>>>> P.S. I wish I could attend the DAS workshop this year and show you what >>>>>>> we've >>>>>>> been up to. Any chance of getting a Skype conference call with posted >>>>>>> presentations? Would be great if someone hosted a DAS Workshop in the >>>>>>> US. >>>>>>> >>>>>>> >>>>>>> On 2/4/11 8:19 AM, "Gregg Helt" <[email protected]> wrote: >>>>>>> >>>>>>> The core genomancer code is pretty stable, most of the recent work is >>>>>>> in plugins (and some work in the core to allow more extensive >>>>>>> plugins). >>>>>>> >>>>>>> You should be able to get a working DAS1-->DAS2 proxy running from >>>>>>> the current head of the Trellis SVN repository -- you would just need >>>>>>> to add a web.xml config file with servlet parameters to get it going in >>>>>>> a >>>>>>> servlet container like Tomcat, or alternatively run the built-in Jetty >>>>>>> server >>>>>>> (ExampleJettyDas2Server) and edit servlet parameters directly in code. >>>>>>> >>>>>>> But if the intent is to load DAS 1.x data into IGB, I don't think you >>>>>>> need to use Trellis. Th latest IGB (6.4.1 loaded via WebStart) >>>>>>> already supports DAS 1.5 access. In the "Data Access" tab, under >>>>>>> "Choose Data Sources and Data Sets" section click the "Configure" >>>>>>> button. This brings up a window with a "Data Sources" tab, and in >>>>>>> that tab you can click the "Add" button to bring up a dialog that lets >>>>>>> you select "DAS" for the data source type, and enter the URL for a DAS >>>>>>> server. This worked fine for loading data from the UCSC DAS 1.5 >>>>>>> server -- I haven't tried accessing data from any other DAS servers >>>>>>> recently. >>>>>>> >>>>>>> I'm forwarding to the genoviz-devel list for IGB developments and >>>>>>> discussion, to see if anyone currently working on IGB can add any more >>>>>>> info. >>>>>>> >>>>>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter >>>>>>> <[email protected]> wrote: >>>>>>>> >>>>>>>> Hi all (but Gregg in particular!) >>>>>>>> >>>>>>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy >>>>>>>> in the Genomancer project (http://code.google.com/p/genomancer/) is >>>>>>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and >>>>>>>> it looks like there's a moderate amount of commit activity in the >>>>>>>> project at the moment, making me a little nervous about attempting to >>>>>>>> use the code in a production(ish) setting. >>>>>>>> >>>>>>>> many thanks in advance, >>>>>>>> Jim. >>>>>>>> >>>>>>>> -- >>>>>>>> ------------------------------------------------------------------- >>>>>>>> J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group >>>>>>>> Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk >>>>>>>> The University of Dundee is a Scottish Registered Charity, No. >>>>>>>> SC015096. >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> DAS mailing list >>>>>>>> [email protected] >>>>>>>> http://lists.open-bio.org/mailman/listinfo/das >>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> DAS mailing list >>>>>>> [email protected] >>>>>>> http://lists.open-bio.org/mailman/listinfo/das >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> DAS mailing list >>>>>>> [email protected] >>>>>>> http://lists.open-bio.org/mailman/listinfo/das >>>>>> >>>>>> >>>>>> >>>>>> >>>> ---------------------------------------------------------------------------- >>>> ->> >>>> - >>>>>> The modern datacenter depends on network connectivity to access resources >>>>>> and provide services. The best practices for maximizing a physical >>>>>> server's >>>>>> connectivity to a physical network are well understood - see how these >>>>>> rules translate into the virtual world? >>>>>> http://p.sf.net/sfu/oracle-sfdevnlfb >>>>>> _______________________________________________ >>>>>> Genoviz-devel mailing list >>>>>> [email protected] >>>>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel >>>>> >>>>> -- >>>>> Ann Loraine >>>>> Associate Professor >>>>> Dept. of Bioinformatics and Genomics, UNCC >>>>> North Carolina Research Campus >>>>> 600 Laureate Way >>>>> Kannapolis, NC 28081 >>>>> 704-250-5750 >>>>> www.transvar.org >>>>> >>>>> >>>>> >>>> >>>> -- >>>> Ann Loraine >>>> Associate Professor >>>> Dept. of Bioinformatics and Genomics, UNCC >>>> North Carolina Research Campus >>>> 600 Laureate Way >>>> Kannapolis, NC 28081 >>>> 704-250-5750 >>>> www.transvar.org >>>> >>>> >>>> >>>> ---------------------------------------------------------------------------- >>>> -- >>>> The modern datacenter depends on network connectivity to access resources >>>> and provide services. The best practices for maximizing a physical server's >>>> connectivity to a physical network are well understood - see how these >>>> rules translate into the virtual world? >>>> http://p.sf.net/sfu/oracle-sfdevnlfb >>>> _______________________________________________ >>>> Genoviz-devel mailing list >>>> [email protected] >>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel >>>> >>>> >>>> _______________________________________________ >>>> DAS mailing list >>>> [email protected] >>>> http://lists.open-bio.org/mailman/listinfo/das >>> >> > > -- > Ann Loraine > Associate Professor > Dept. of Bioinformatics and Genomics, UNCC > North Carolina Research Campus > 600 Laureate Way > Kannapolis, NC 28081 > 704-250-5750 > www.transvar.org > > _______________________________________________ DAS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/das
